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. 2018 Feb 13;5:15. doi: 10.3389/fmolb.2018.00015

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Copyright © 2018 Milton, Minrovic, Harris, Kang, Jung, Lewis, Thompson, Melander, Zeng, Melander and Cavanagh.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Population distribution of PmrA. Having started with an “extended” state, the populations shifts to predominately “tucked” on a short time scale. (A) Molecular dynamics of PmrA (PDB ID 4S05) quickly relaxes to a “tucked/tucked” state and samples this state 76% of the time at a 250 ns time scale. (B) The PmrA crystal structure bound to DNA (center) begins in a “tucked/extended” state. Variations on the “tucked/extended” state are sampled for very short periods of time and account for small portions of the population at a given time. Structure models represent the top scoring pose from each cluster based on free energy minimization.